Package org.pathvisio.libgpml.model

Class PathwayElement.EvidenceRef

java.lang.Object
org.pathvisio.libgpml.model.PathwayElement.InfoRef
org.pathvisio.libgpml.model.PathwayElement.EvidenceRef
Enclosing class:
PathwayElement
public class PathwayElement.EvidenceRef
extends PathwayElement.InfoRef
This class stores information for a EvidenceRef which references an Evidence.
Author:
finterly

  • Field Details

  • Constructor Details

    • EvidenceRef

      protected EvidenceRef​(Evidence evidence)
      Instantiates an EvidenceRef given source Evidence and initializes evidenceRefs lists.
      Parameters:
      evidence - the source evidence this EvidenceRef refers to.

  • Method Details

    • getEvidence

      public Evidence getEvidence()
      Returns the evidence referenced.
      Returns:
      evidence the evidence referenced.

    • hasEvidence

      public boolean hasEvidence()
      Checks whether this evidenceRef has a source evidence.
      Returns:
      true if and only if the evidence of this evidenceRef is effective.

    • setEvidenceTo

      public void setEvidenceTo​(Evidence evidence)
      Sets the source evidence for this evidenceRef. Adds this evidencRef to the source evidence.
      Parameters:
      evidence - the given source evidence to set.

    • setEvidence

      private void setEvidence​(Evidence v)
      Sets the source evidence for this evidenceRef.
      Parameters:
      v - the given source evidence to set.

    • unsetEvidence

      public void unsetEvidence()
      Unsets the evidence, if any, from this evidenceRef. Removes this evidenceRef from the source evidence.

    • getEvidenceable

      public Referenceable.Evidenceable getEvidenceable()
      Returns the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable for this evidenceRef.
      Returns:
      evidenceable the target of the evidenceRef.

    • hasEvidenceable

      public boolean hasEvidenceable()
      Checks whether this evidenceRef has a target evidenceable.
      Returns:
      true if and only if the evidenceable of this evidenceRef is effective.

    • setEvidenceableTo

      protected void setEvidenceableTo​(Referenceable.Evidenceable evidenceable)
      Sets the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable for this evidenceRef. NB: Evidenceable is only set when an Evidenceable adds a EvidenceRef. This method is not used directly.
      Parameters:
      evidenceable - the given target evidenceable to set.

    • setEvidenceable

      private void setEvidenceable​(Referenceable.Evidenceable v)
      Sets the target pathway, pathway element, or evidenceRef Referenceable.Evidenceable to which the evidenceRef belongs.
      Parameters:
      v - the given target evidenceable to set.

    • unsetEvidenceable

      protected void unsetEvidenceable()
      Unsets the evidenceable, if any, from this evidenceRef. NB: This method is not used directly.

    • terminate

      protected void terminate()
      Terminates this evidenceRef. The evidence and evidenceable, if any, are unset from this evidenceRef. Links to all evidenceRefs are removed from this evidenceRef.

    • toString

      public java.lang.String toString()
      Writes evidenceRef out as string.
      Overrides:
      toString in class java.lang.Object